Designing Multiple Simultaneous Seeds for DNA Similarity Search. - Yanni Sun; Jeremy Buhler (J. Comput. Biol., 2005)

Designing seeds for similarity search in genomic DNA. - Jeremy Buhler; Uri Keich; Yanni Sun (J. Comput. Syst. Sci., 2005)

Choosing the best heuristic for seeded alignment of DNA sequences. - Yanni Sun; Jeremy Buhler (BMC Bioinform., 2006)

Designing patterns for profile HMM search. - Yanni Sun; Jeremy Buhler (Bioinform., 2007)

Designing Patterns and Profiles for Faster HMM Search. - Yanni Sun; Jeremy Buhler (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

BLAST Tree: Fast Filtering for Genomic Sequence Classification. - Stuart King; Yanni Sun; James R. Cole; Sakti Pramanik (BIBE, 2010)

NcRNA homology search using Hamming distance seeds. - Osama Aljawad; Yanni Sun; Alex Liu; Jikai Lei (BCB, 2011)

HMM-FRAME: accurate protein domain classification for metagenomic sequences in the presence of frameshift errors. - Yuan Zhang; Yanni Sun (BMC Bioinform., 2011)

Ncrna Consensus Secondary Structure Derivation Using Grammar Strings. - Rujira Achawanantakun; Yanni Sun; Seyedeh Shohreh Takyar (J. Bioinform. Comput. Biol., 2011)

PseudoDomain: identification of processed pseudogenes based on protein domain classification. - Yuan Zhang; Yanni Sun (BCB, 2012)

MetaDomain: A Profile HMM-Based Protein Domain Classification Tool for Short Sequences. - Yuan Zhang; Yanni Sun (Pacific Symposium on Biocomputing, 2012)

Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy. - Yanni Sun; Osama Aljawad; Jikai Lei; Alex Liu (BMC Bioinform., 2012)

Designing Filters for Fast-Known NcRNA Identification. - Yanni Sun; Jeremy Buhler; Cheng Yuan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools. - Jikai Lei; Prapaporn Techa-angkoon; Yanni Sun; Rujira Achawanantakun (BCB, 2013)

glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity. - Prapaporn Techa-angkoon; Yanni Sun (BCB, 2013)

A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads. - Yuan Zhang; Yanni Sun; James R. Cole (Bioinform., 2013)

Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM. - Rujira Achawanantakun; Yanni Sun (BMC Bioinform., 2013)

Efficient known ncRNA search including pseudoknots. - Cheng Yuan 001; Yanni Sun (BMC Bioinform., 2013)

Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm. - Jikai Lei; Prapaporn Techa-angkoon; Yanni Sun (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data. - Jikai Lei; Yanni Sun (Bioinform., 2014)

Ribosomal Database Project: data and tools for high throughput rRNA analysis. - James R. Cole; Qiong Wang; Jordan A. Fish; Benli Chai; Donna M. McGarrell; Yanni Sun; C. Titus Brown; Andrea Porras-Alfaro; Cheryl R. Kuske; James M. Tiedje (Nucleic Acids Res., 2014)

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data. - Yuan Zhang; Yanni Sun; James R. Cole (PLoS Comput. Biol., 2014)

LncRNA-ID: Long non-coding RNA IDentification using balanced random forests. - Rujira Achawanantakun; Jiao Chen 002; Yanni Sun; Yuan Zhang (Bioinform., 2015)

Reconstructing 16S rRNA genes in metagenomic data. - Cheng Yuan 001; Jikai Lei; James R. Cole; Yanni Sun (Bioinform., 2015)

Improve homology search sensitivity of PacBio data by correcting frameshifts. - Nan Du 003; Yanni Sun (Bioinform., 2016)

Assemble CRISPRs from metagenomic sequencing data. - Jikai Lei; Yanni Sun (Bioinform., 2016)

Computer Network Simulation Modeling Based on Object Oriented Petri Net. - Xinhua Chen; Yanni Sun (Int. J. Online Eng., 2016)

Application and Realization of Improved Apriori Algorism in Hadoop Simulation Platform for Mass Data Process. - Yanni Sun; Xinhua Chen (Int. J. Online Eng., 2016)

A sensitive short read homology search tool for paired-end read sequencing data. - Prapaporn Techa-angkoon; Yanni Sun; Jikai Lei (BMC Bioinform., 2017)

Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse. - Jiao Chen 002; Dongxiao Zhu; Yanni Sun (Quant. Biol., 2017)

De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding. - Jiao Chen 002; Yingchao Zhao 001; Yanni Sun (Bioinform., 2018)

TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data. - Jiao Chen 002; Jiating Huang; Yanni Sun (BMC Bioinform., 2019)

A binning tool to reconstruct viral haplotypes from assembled contigs. - Jiao Chen 002; Jiayu Shang; Jianrong Wang; Yanni Sun (BMC Bioinform., 2019)

Fast and accurate microRNA search using CNN. - Xubo Tang; Yanni Sun (BMC Bioinform., 2019)

GPRED-GC: a Gene PREDiction model accounting for 5 ′- 3′ GC gradient. - Prapaporn Techa-angkoon; Kevin L. Childs; Yanni Sun (BMC Bioinform., 2019)

Improving the sensitivity of long read overlap detection using grouped short k-mer matches. - Nan Du 003; Jiao Chen 002; Yanni Sun (BMC Genom., 2019)

The Lung Cancer Associated MicroRNAs and Single Nucleotides Polymorphisms: a Mendelian Randomization Analysis. - Ruixuan Huang; William C. Cho; Yanni Sun; Kei Hang Katie Chan (EMBC, 2020)

ProDOMA: improve PROtein DOMAin classification for third-generation sequencing reads using deep learning. - Nan Du 003; Jiayu Shang; Yanni Sun (CoRR, 2020)

Bacteriophage classification for assembled contigs using graph convolutional network. - Jiayu Shang; Jingzhe Jiang; Yanni Sun (Bioinform., 2021)

Detecting the hosts of bacteriophages using GCN-based semi-supervised learning. - Jiayu Shang; Yanni Sun (CoRR, 2021)

CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model. - Jiayu Shang; Yanni Sun (Briefings Bioinform., 2022)

Accurate identification of bacteriophages from metagenomic data using Transformer. - Jiayu Shang; Xubo Tang; Ruocheng Guo; Yanni Sun (Briefings Bioinform., 2022)

RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data. - Xubo Tang; Jiayu Shang; Yanni Sun (Briefings Bioinform., 2022)

Reconstructing viral haplotypes using long reads. - Dehan Cai; Yanni Sun (Bioinform., 2022)

HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization. - Dehan Cai; Jiayu Shang; Yanni Sun (Bioinform., 2022)

Research on the Method Matching of Manufacturing Service Resources in a Cloud Manufacturing Environment. - Yanni Sun; Baohua Yu (ICCAI, 2023)

PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer. - Jiayu Shang; Cheng Peng 020; Xubo Tang; Yanni Sun (Bioinform., 2023)

Virus classification for viral genomic fragments using PhaGCN2. - Jingzhe Jiang; Wen-Guang Yuan; Jiayu Shang; Ying-Hui Shi; Li-Ling Yang; Min Liu; Peng Zhu; Tao Jin; Yanni Sun; Li-Hong Yuan (Briefings Bioinform., 2023)

PhaTYP: predicting the lifestyle for bacteriophages using BERT. - Jiayu Shang; Xubo Tang; Yanni Sun (Briefings Bioinform., 2023)

AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data. - Runzhou Yu; Dehan Cai; Yanni Sun (Bioinform., 2023)

VirBot: an RNA viral contig detector for metagenomic data. - Guowei Chen; Xubo Tang; Mang Shi; Yanni Sun (Bioinform., 2023)

HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer. - Yongxin Ji; Jiayu Shang; Xubo Tang; Yanni Sun (Bioinform., 2023)

PhaGenus: genus-level classification of bacteriophages using a Transformer model. - Jiaojiao Guan; Cheng Peng 020; Jiayu Shang; Xubo Tang; Yanni Sun (Briefings Bioinform., 2023)

HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses. - Runzhou Yu; Syed Muhammad Umer Abdullah; Yanni Sun (Briefings Bioinform., 2023)

GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data. - Herui Liao; Jiayu Shang; Yanni Sun (Bioinform., 2023)

GOPhage: protein function annotation for bacteriophages by integrating the genomic context. - Jiaojiao Guan; Yongxin Ji; Cheng Peng 020; Wei Zou; Xubo Tang; Jiayu Shang; Yanni Sun (Briefings Bioinform., 2024)

Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review. - Runzhou Yu; Ziyi Huang; Theo Y. C. Lam; Yanni Sun (Briefings Bioinform., 2024)

Towards more accurate microbial source tracking via non-negative matrix factorization (NMF). - Ziyi Huang; Dehan Cai; Yanni Sun (Bioinform., 2024)

SmoothGNN: Smoothing-based GNN for Unsupervised Node Anomaly Detection. - Xiangyu Dong 002; Xingyi Zhang 003; Yanni Sun; Lei Chen 031; Mingxuan Yuan; Sibo Wang 001 (CoRR, 2024)

PhaGO: Protein function annotation for bacteriophages by integrating the genomic context. - Jiaojiao Guan; Yongxin Ji; Cheng Peng 020; Wei Zou; Xubo Tang; Jiayu Shang; Yanni Sun (CoRR, 2024)

SmoothGNN: Smoothing-aware GNN for Unsupervised Node Anomaly Detection. - Xiangyu Dong 002; Xingyi Zhang 003; Yanni Sun; Lei Chen 031; Mingxuan Yuan; Sibo Wang 001 (WWW, 2025)

SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples. - Xue Liu; Jianbin Kong; Yongtao Shan; Ziyue Yang; Jiafan Miao; Yuanfei Pan; Tianyang Luo; Zhiyuan Shi; Yingmei Wang; Qinyu Gou; Chunhui Yang; Hanzong Li; et al. (Briefings Bioinform., 2025)